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VIOLIN & VO

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VO in VIOLIN

Vaccine Ontology (VO) User Cases and Groups

     We have already had many VO user cases and user groups:

1. VO-based Natural Lanuge Processing (NLP): Ontology-based NLP allows more accurate performance on literature mining. VIOLIN is collaborating with the National Center for Integrative Biomedical Informatics (NCIBI) led by Drs. Brian Athey and Gil Omenn to develop VO-based NLP tool to enhance vaccine literature mining.
2. VO-based Immune Response Network: VIOLIN is working with NCIBI to develop a VO-based immune response network system for study of protective immune responses against infectious diseases. Brucella (domain expert: Dr. Oliver He) and E. coli (domain expert: Dr. Harry Mobley) have been chosen as user cases for this system development.
3. Vaccine Semantic Web: Simply speaking, the Semantic Web is a way to make computers understand computers. Ontologies are the foundations for the Semantic Web. VIOLIN is collabarating with Alan Ruttenberg from Science Commons to develop a vaccine-oriented Semantic Web system using VO and other ontologies.
4. Integration of VO with OBI: Many VO terms (e.g., vaccination) are related to various vaccine experiments that may be the coverage domains of the Ontology for Biomedical Investigations (OBI). Vaccine research has provided user case studies for OBI development. Many members in the VO team are also part of the OBI Consortium (e.g., Dr. Bjeorn Peters, Dr. Richard Scheuermann, and Alan Ruttenberg). We will ensure synergistic development of VO and OBI.
5. Application of VO in Epitope-related Modeling: Immune dominant epitopes are critical for vaccine development. Dr. Bjoern Peters (La Jolla Institute for Allergy and Immunology), the bioinformatics leader of the Immune Epitope Database project (http://www.immuneepitope.org), is interested in using VO for epitope/immunology related computational modeling.
6. Application of VO in Developtment of Influenza Ontology (InfluenzO): InfluenzO is an influenza application ontology that references more than 10 other ontologies. Dr. Richard Scheuermann (University of Texas Southwestern Medical Center), a member of the InfluenzO Consortium, is interested in applying VO in InfluenzO.
7. University of Michigan Vaccine Informatics and Resource Advisory Committee (VIRAC): a group of professors in Michigan is seeking to use the VO for their various research interests. Examples of the VIRAC research activities include:
   • Dr. Oliver He's lab is analyzing the interactions between host and Brucella vaccines. Dr. He is interested in using the VO to study differential immune responses induced by Brucella vaaccines (e.g., RB51 and Strain 19) in various hosts (e.g., human, cattle, and mouse).
   • Dr. Harry Mobley's lab is developing subunit vaccines against urinary tract infection (UTI) caused by uropathogenic Escherichia coli (UPEC) using reverse vaccinology. Dr. Mobley is interested in applying the VO for vaccine target prediction and study of immune mechansim and potential pathogenesis of protective antigens.
   • Dr. Zhenhua Yang's lab is studying DNA polymorphisms in genes used for TB vaccine development (e.g., pepA and PPE18) among clinical strains of Mycobacterium tuberculosis (See reference: PMID: 17893137). Dr. Yang is interested in using the VO to organize and analyze vaccine gene polymorphisms.

     We welcome more users to join our VO user groups with more VO-based case studies and examples.